Zuma’s office has rejected requests to release the document, saying it did not exist as the generals commissioned by former president Thabo Mbeki to investigate abuses never reported to him in writing.
Piers Pigou, the director of the SA History Archives (SAHA), said he believed the presidency was lying.
"It makes no sense that these people would provide Mbeki with only oral testimony. We think the presidency is setting itself up to be questioned. It is very sad."
Pigou said though violence and fear levels in Zimbabwe had since decreased, light should be shed on last year’s rein of terror to prompt a transformation of the military and prevent future abuses.
Human rights groups accused President Robert Mugabe of unleashing a systematic campaign of violence on opposition supporters after his Zanu-PF lost control of Parliament to the Movement for Democratic Change in elections in March 2008.
MDC leader Morgan Tsvangirai claimed at least 100 of his supporters were killed.
Mbeki, the Southern African Development Community’s mediator in Zimbabwe, in May last year tasked six retired generals to assess the extent of the army’s involvement in the political crisis.
The generals conducted fact-finding missions in May and June but Mbeki never released their findings. Neither did his successor, Kgalema Motlanthe.
The SAHA, the Southern Africa Litigation Centre and the SA Centre for Survivors of Torture as well as the Democratic Alliance have invoked the Promotion of Access to Information Act to force Zuma to release the document.
But Pigou said Frank Chikane, the director general in the presidency under Mbeki, and Trevor Fowler, who currently holds the post, produced affidavits saying no report or supporting documentation exits and the generals reported only orally to Mbeki.
The NGOs insist however that the generals produced a report that painted a "devastating" picture of state-sponsored violence that shifted Mbeki’s perceptions on the situation in Zimbabwe.
"The report is believed to have been hard-hitting and instrumental in the evolution of subsequent negotiations leading to the September Global Political Agreement" on power-sharing between Zanu-PF and the MDC, they said in a statement.
The DA’s parliamentary leader Athol Trollip said on Thursday he has had no formal reply to his application but would find it "very difficult to believe and even unacceptable" that the generals had not produced a written report.
Trollip said he had been told by a human rights activist interviewed by the generals that they handed Mbeki a thorough and "hard-hitting" report on state-sponsored violence.
The NGOs said Zuma should send the generals back to probe reports of continued intimidation and harassment by Zimbabwean security and intelligence forces intended to undermine the country’s fragile unity government formed in February. (Sapa)